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MANCHESTER — Investigators quickly concluded Sunday that an overnight fire in a building that has stood for more than a century on the campus of a state juvenile corrections center was set intentionally.

The fire destroyed much of the roof and caused significant damage to the third floor of the “Wilkins Cottage,” the northernmost building on the state-owned property that has been home to New Hampshire youth reform efforts since the 1850s.

The three-story building, built as a girls' dormitory in the early 1900s, has been vacant for nearly 40 years; it is set apart from the buildings currently in use at the John H. Sununu Youth Services Center.

“There was really nothing to it but a vacant shell. It was heavily involved in fire when we arrived,” Manchester Fire District Chief Mike Gamache said.

The call came in around 2 a.m. as the flames roared high above the historic structure; firefighters battled the blaze for several hours. Gamache said the task was made more difficult because the building has been boarded up tightly for years. The wooden panels covering the south face of the building were still in place late Sunday morning after the last of the firefighters left around 9:20 a.m.

Gamache said there was evidence at the scene that the fire had been “maliciously set,” but would not elaborate. The Manchester Fire Marshal’s Office and Police Department are investigating.

Fire officials estimated damage at $250,000.

Wilkins is on its own cul-de-sac, almost hidden behind an expanse of trees and overgrowth. The remote location of the building was an issue when the nearest hydrant wasn’t supplying enough water. Firefighters had to run 5-inch hoses to other hydrants, eventually laying 3,000 feet of hose, District Chief Mark Pelletier said in a news release.

Hoses also stretched east to River Road for additional water needed to extinguish the fire, which was declared under control at 5:30 a.m.

The building had no electricity or other utilities, fire officials said.

The 144-bed John H. Sununu Center, commonly referred to by its previous name of the Youth Development Center, stands on land that was once the farm of Gen. John Stark. Manchester lawyer, politician and youth advocate James McKeen Wilkins bequeathed it to the state when he died in 1855.

The only stipulation was that the state use the property for a reform school, which Wilkins felt was a better and less severe option than adult prison.

According to a YDC assessment study in 2006, the 25,000-square-foot building that bears Wilkins’ name remained in use until it was closed in 1976-77. It fell into disrepair over the decades as the state considered options.

The state property still has some agricultural ties, with New Hampshire Food Bank vegetable gardens and stables that housed the Manchester Police Department horses.

The Sununu Center is part of the state Department of Health and Human Services. Department spokeswoman Kris Neilsen said Sunday that the state had maintained the historic structure, but there were no plans for renovations.